A compiled program written in C# or any other similar low level language will always be faster than a Perl script IF it is written correctly. If the programmer didn't code it correctly, the program, no matter which language it was written in, would be efficient/fast.

Without knowing anything about your current program and parsing details I can't say for sure if a Perl script can process your files any faster, but several hours for a C# program does sound like it may not have been coded correctly.